This is a philosophical argument in terms of a challenge to justify God’s actions and as such falls outside scientific proof (The challenge is philosophical, so the defense must necessarily also be).
Firstly - God is the creator according to the bible (an attack on the bible must logically be defensible from the bible – otherwise the challenge is meaningless). Israel’s moral duties are constituted by God's commands. He is under no obligation to extend life and is not subject to the same moral obligations and prohibitions as the Israelites. Does this mean that God commanded the Israelites to commit murder? Not in this case, it would only be classified as murder (put in any of the Israeli actions against Canaan) if done in the absence of Divine command (William Lane Craig’s defense used and accompanying refutations considered – the existence of a refutation does not automatically mean the initial statement is incorrect).
Genesis indicates that God had reasons for commanding the destruction of the Canaanites (includes Abrahams haggling with God regarding the salvation of Sodom & Gomorrah (Gen 18) and the 400 years that God delayed his judgment (Gen 15) of the Canaanites). The Canaanite culture was not good (As the lawgiver and omniscient being – He would judge best what is good and what is not) according to God (He gave reasons why He did not regard them as good).
He knew exactly the course of action that anyone of the Canaanites would take if they stayed alive (including the babies):
For the adults it was punishment for their actions – A person with a naturalistic view might judge it as harsh and genocidal because all the information God had at his disposal is not available or is not accepted (God’s infinitely good nature) - Similar to a cleaner judging the decision of the CEO without all the information or understanding, as applicable.
Please also note that genocide (mass murder ala Pol Pot etc.) will always be wrong as that is how God defined it. God’s judgment is however not genocide (Defined as such due to a deficient understanding or non-acceptance of God’s nature) in a similar way that a judge giving a serial killer the death penalty is not classified as murder. The Israelites are not murderers in a similar way that an executioner carrying out the death penalty (according to law, not outside of it) is not a murderer. It would be regarded as Genocide from an atheist point of view due to the belief that earth and the seen universe is all there is. God would have turned from His anger if the Canaanites turned from their ways (City of Nineveh, Jonah 3). Israel themselves was also judged for the same sins later in the old Testament – God shows no favoritism.
For the babies - God knew their future and decided it is best that they are taken to heaven – you define it as infanticide for the same reason stated above. In addition, the Bible teaches that there is heaven and hell – heaven being infinitely better than earth and hell being infinitely worse. If God took the babies to Him in heaven, they are in an infinitely better position than they would have been on earth – like child welfare taking a child away from unfit parents. There is archeological proof that babies were sacrificed by the Canaanites themselves (Unger, Archeology and the Old Testament, 279)
Deuteronomy 7:2: The Hebrew term refers to the irrevocable giving over of things or persons to the Lord, often by totally destroying them – biblical premise for above.
In addition I would point out that the methods employed in warfare at the time in question – you will find that it was standard practice to annihilate your enemy instead of the way it works today (ie. The Geneva Convention). It was a question of kill or be killed. God did not command the exact method of killing the babies – the method used was probably standard methods of war in those times. In modern times it will obviously be viewed as atrocious. The value of human life has increased immeasurably since those times (with some exceptions based on modern thinking).
For this reason God is delaying his final judgment to the end of the world instead of punishing us as and when we commit sin (Not many of us would have remained alive very long) if punishment was immediate. The question is, how would you be able to judge were it not for the creation of morals by God? Are you a better judge than the creator of everything?